British Airways announced that its chief executive Alex Cruz is stepping down "with immediate effect".
The airline gave reason for his departure.
Parent group IAG said Mr Cruz, who has been BA chief executive for four and half years, will be replaced by Aer Lingus boss Sean Doyle, but will remain non-executive chairman.
New IAG chief executive Luis Gallego, who took the reins from Willie Walsh last month, said the reshuffle was aimed at emerging stronger from the Covid-19 pandemic, which has greatly reduced demand for air travel.
Mr Cruz is leaving after being passed over in January as replacement for the group’s chief.
Initially seen as a likely successor to Mr Walsh, Mr Cruz, 54, was criticised for the extent of cost cuts and service changes during his four years at the helm. Pilots, former staff and customers suggested British Airways’ image as a premium carrier was being tarnished – even as Mr Walsh kept up pressure for even deeper cutbacks.
"We're navigating the worst crisis faced in our industry and I'm confident these internal promotions will ensure IAG is well placed to emerge in a strong position," Mr Gallego said of Mr Cruz's departure.
"I want to thank Alex for all that he has done at British Airways. He worked tirelessly to modernise the airline in the years leading up to the celebration of its 100th anniversary.
"Since then, he has led the airline through a particularly demanding period and has secured restructuring agreements with the vast majority of employees."
A company spokeswoman declined to comment on media speculation over the nature of his departure.
Mr Cruz gave no comment on his surprise departure.
The Spanish businessman, 54, oversaw painful restructuring at the airline as it counted the cost of the coronavirus crisis.
BA is cutting 13,000 staff and has been roundly criticised by staff and MPs over a "fire and rehire" policy.
Some employees faced pay cuts of up to half their original salary.
Mr Cruz also oversaw the airline's transition to new Brexit arrangements after the UK voted to leave the EU.
The BA pilot strike in 2019, which grounded 1,700 flights, also occurred on his watch, costing the airline £125 million ($163m).
Years of IT problems that stranded thousands of passengers also dogged Mr Cruz's tenure.
When appointed to the job in 2016, he vowed to make BA more cost efficient to allow it to better compete with budget airlines such as RyanAir and EasyJet.
He was previously chief executive at Vueling from 2009 when it merged with Clickair, an airline Mr Cruz founded in 2006.
As coronavirus upended the airline industry this year, Mr Cruz called for an air bridge with the US to open up the lucrative transatlantic route.
Last month he defended heavy job cuts at the airline and argued that customers were "still afraid of travelling".
"Covid has devastated our business, our sector. We're still fighting for our own survival," he told parliament's transport select committee.
IAG has forecast that it will take until at least 2023 for passenger demand to recover to pre-pandemic levels.
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Mr Cruz said: “As CEO of British Airways, I have to take responsibility. I cannot ignore the situation. I had to act incredibly fast.
“I deeply, deeply regret that way too many loyal and hardworking colleagues of mine are having to leave our business, and I understand why MPs are concerned.”
Shares of IAG rose 1.4 per cent in early morning trading after the announcement.
